Hello. I have a Fastq file with 30,000 reads. When I analyze them with Fastqc the level of duplicates goes very high. Then I trim the readings to eliminate low quality bases and the levels of duplicates drop to normal levels. I suppose this will be because when I change the length of the readings the program doesn't consider them as duplicates. Then I map the readings with Bowtie2 and I pass the BAM file to MarkDuplicates. Almost all the sequences are mapped but PERCENT DUPLICATION go back up to 80%. How can this be?
Thank you.